High Specificity HIV-1 Markers Predictive of Neuro-AIDS

描述（由申请人提供）：免疫系统、脑和其他终末器官感染1型人免疫缺陷病毒（HIV-1）后的发病机制和疾病进展依赖于病毒进入这些区室中的特定细胞群并在其中复制，通过多种直接和/或间接机制导致细胞功能障碍或死亡。这些病毒-宿主相互作用可由许多因素调节，包括病毒结合和进入、宿主细胞增殖和活化、细胞分化、抗逆转录病毒治疗状态、滥用物质以及与长末端重复序列（LTR）相互作用以调节病毒表达的病毒和细胞蛋白的作用。HIV-1的复制能力进一步受到病毒准种进化的影响。研究表明，LTR内天然存在的序列变异通过改变与细胞和病毒反式激活因子的功能相互作用来影响病毒启动子驱动病毒表达的能力。最近的研究表明，HIV-1基因组内的遗传改变可能与HIV-1疾病的阶段、神经系统状态和/或器官区室化相关。然而，这些研究中的许多研究涉及HAART前时期少量患者的临床样本的交叉人群分析，而不是HAART时期具有足够患者数量的纵向研究。拟议的研究将利用不断扩大的DREXELMED HIV- 1感染患者队列进行交叉人群和纵向研究，以进行测序和结构/功能分析，以检查工作假设，即LTR和病毒包膜内的结合位点签名可用作分子标记物，以识别更容易发展为晚期疾病的HIV-1感染个体，器官受累，可能因特定的合并症如可卡因或大麻素滥用而加重。本申请的具体目的是继续：（1）构建HIV-1来源于外周血单核细胞（PBMC）的（亚型B）LTR和Env聚合酶链反应（PCR）产物序列数据库和克隆库从具有全面社会和临床人口统计学临床病史的患者中纵向收集的HIV-1感染外周血（PB）（初始和所有回访），（2）鉴定LTR和Env单核苷酸多态性（SNP）和在来源于PBMC的LTR中检测到的共同选择的SNP（csSNP）[以及，在选定的情况下，纯化的PB亚群，血浆病毒，CNS组织（NNTC）和其它细胞区室]，其使用生物信息学工具从大量充分研究的HIV-1感染的队列中获得，以检查HIV-1 LTR的634个核苷酸中的任一个处、HIV-1 gp 120内或HIV-1 gp 41内的SNP，（3）构建平行PCR产物序列数据库，并从具有不同程度的HIV-1相关神经系统疾病的脑组织中定义特异性LTR和Env SNP和csSNP，所述脑组织从国家神经系统疾病研究所获得。AIDS Tissue Consortium（NNTC）]，和（4）确定含有特异性csSNP的HIV-1 LTR克隆支持转录和病毒复制研究的能力。

DESCRIPTION (provided by applicant): Pathogenesis and disease progression subsequent to human immunodeficiency virus type 1 (HIV-1) infection of the immune system, brain, and other end organs is dependent on viral entry and replication in specific cell populations within these compartments that cause celular dysfunction or death by a variety of direct and/or indirect mechanisms. These virus-host interactions can be regulated by numerous factors, including viral binding and entry, host cell proliferation and activation, cellular differentiation, antiretroviral therapy status, substances of abuse, and the action of viral and cellular proteins that interface with the long terminal repeat (LTR) and to each other to regulate viral expression. The capacity of HIV-1 to replicate is further affected by the evolution of viral quasispecies. Studies have indicated that naturally-occurring sequence variation within the LTR influences the ability of the viral promoter to drive viral expression by altering functional interactions with cellular and viral trans-activators. Recent studies have suggested the possibility that genetic alterations within the HIV-1 genome may correlate with either the stage of HIV-1 disease, neurologic status, and/or organ compartmentalization. However, many of these studies involved cross population analyses of clinical samples from a small number of patients in the pre-HAART era, rather than from longitudinal studies with sufficient patient numbers in the HAART era. The proposed studies will utilize a continually expanding DREXELMED HIV- 1-infected patient cohort for cross-population and longitudinal studies for sequencing and structure/function analyses to examine the working hypothesis that binding site signatures within the LTR and viral envelope can be used as molecular markers to identify HIV-1-infected individuals more prone to developing advanced stage disease with end-organ involvement that may be exacerbated by specific co-morbidities such as cocaine or cannabinoid abuse The specific aims of this application are to continue to: (1) construct a HIV-1 (subtype B) LTR and Env polymerase chain reaction (PCR) product sequence database and clone bank derived from peripheral blood mononuclear cells (PBMCs) from HIV-1-infected peripheral blood (PB) collected longitudinally from patients with comprehensive clinical histories with respect to social and clinical demographics (initial and all return visits), (2) identify LTR and Env single nucleotide polymorphisms (SNPs) and co-selected SNPs (csSNPs) detected in LTRs derived from PBMCs [and, in selected circumstances, purified PB sub-populations, plasma virus, CNS tissues (NNTC) and other cellular compartments] obtained from a large well studied HIV-1- infected cohort using bioinformatic tools to examine SNPs at any of the 634 nucleotides of the HIV-1 LTR, within the HIV-1 gp120, or within the HIV-1 gp41, (3) construct a parallel PCR product sequence database and define specific LTR and Env SNPs and csSNPs from brain tissues with varying degrees of HIV-1-associated neurologic disorders obtained from the National Neuro-AIDS Tissue Consortium (NNTC)], and (4) determine the ability of HIV-1 LTR clones containing specific csSNPs to support transcription and viral replication studies.